Engineering bacterial behaviors to control microbiota invasion resistance

项目摘要/摘要(项目1) 人和其他动物的胃肠道微生物区系，由大量单个细胞组成 代表了许多不同的物种，充当了一个虚拟器官，有助于广泛的生理 流程。与大多数器官相比，它更容易受到强烈而频繁的干扰，因为它与 外部世界和物种间的竞争本质上是一个多物种联盟。这些 干扰可以是化学的，例如来自抗生素药物的，也可以是生物的，例如来自新物种的入侵，以及 可能与微生物的运动和空间分布等物理特征有关。很可能是因为 人类微生物组组成的巨大变异性，无论是在个人内部还是在不同时间之间 群体中的个体，部分是由于对外部驱动刺激的变化的反应。尽管如此， 我们对特定扰动如何影响肠道微生物群落的理解，以及是否通用 功能可能会统一不同的反应，仍然是最小的。我们提出了一系列实验，以解决 这项研究以斑马鱼幼体为模型宿主-微生物系统。斑马鱼仔鱼对诺和菌素的适应性 操纵使大量复制群体及其光学透明度的受控实验成为可能 允许对微生物丰度、空间分布和动态进行基于成像的量化。我们专注于 关于两类重要的扰动：新物种的入侵和抗生素的暴露。这个 新物种的引入是肠道环境的一个恒定特征，而运动等行为 趋化性可能在寄生微生物和入侵微生物之间的相互作用中发挥重要作用。建房 在合成生物学的进展方面，我们将设计基因开关来报告和控制这些行为 利用占优势的斑马鱼提供的控制来操纵肠道群落。抗生素的使用是 从元基因组学研究中已知，即使在低水平(亚基因组学)，也会显著影响胃肠道微生物区系 致命性)剂量，原因尚不清楚。根据初步数据，我们假设甚至 微弱的抗生素干扰可以显著改变细菌的行为、空间分布和持久性。 在肠道内，改变物种丰富度并向新宿主扩散。我们提议的实验将 提供有关常见扰动如何影响肠道微生物区系动态的新见解 为了解健康和疾病期间人类微生物群的动态奠定基础。

PROJECT SUMMARY/ABSTRACT (PROJECT 1) The gastrointestinal microbiota of humans and other animals, composed of vast numbers of individual cells representing many different species, serves as a virtual organ contributing to a wide range of physiological processes. More than most organs, it is subject to strong and frequent perturbations due to its connectedness to the outside world and the inter-species competition inherent in its nature as a multi-species consortium. These perturbations may be chemical, e.g. from antibiotic drugs, or biological, e.g. from invasion by new species, and may couple to physical characteristics of microbes such as motility and spatial distribution. It is likely that the large variability in human microbiome composition, both within individuals over time and between individuals in populations, is due in part to responses to variations in externally driven stimuli. Despite this, our understanding of how specific perturbations influence gut microbial communities, and whether generic features might unify diverse responses, remains minimal. We propose a series of experiments that will address this, using larval zebrafish as a model host-microbe system. The amenability of larval zebrafish to gnotobiotic manipulation enables controlled experiments with large replicate populations, and their optical transparency allows imaging-based quantifications of microbial abundances, spatial distributions, and dynamics. We focus on two important classes of perturbations: invasion by new species and exposure to antibiotics. The introduction of new species is a constant feature of the intestinal environment, and behaviors such as motility and chemotaxis likely play important roles in interactions between resident and invasive microbes. Building on advances in synthetic biology, we will engineer genetic switches to report on and control these behaviors in situ, using the control afforded by gnotobiotic zebrafish to manipulate intestinal communities. Antibiotic use is known from metagenomic studies to dramatically affect the gastrointestinal microbiota, even at low (sub- lethal) doses, for reasons that remain to be discovered. Building on preliminary data, we hypothesize that even weak antibiotic perturbations can dramatically alter bacterial behaviors, spatial distributions, and persistence within the gut, altering both species abundances and dispersal to new hosts. Our proposed experiments will provide new insights into how common perturbations influence intestinal microbiota dynamics and will establish a foundation for understanding the dynamics of human microbiomes during both health and disease.